Neuroinformatics support tools: XooNIps, Concierge, Samurai Graph and 3D-SE Viewer

Abstract

Event Abstract Back to Event Neuroinformatics support tools: XooNIps, Concierge, Samurai Graph and 3D-SE Viewer Shiro Usui1*, Yoshihiro Okumura1, Takayuki Kannon1 and Liuji N. Kamiji1 1 RIKEN Brain Science Institute, Tokyo, Japan The Laboratory for Neuroinformatics at RIKEN Brain Science Institute was established in 2002 with the aim of developing essential technologies for further promotion and support to understand the brain in the IT era. We have developed several neuroinformatics tools to contribute to the advancement of this field in Japan. XooNIps is a Neuroinformatics base-platform system which can be utilized from personal use, to small groups such as laboratories, up to a large community like public platforms. The flexibility of XooNIps is further demonstrated by its user for the development of organizational repositories of libraries and research institutions. XooNIps has also gained popularity among private companies due to its easy to use interface compared to similar tools such as D-Space. RIKEN is also considering the XooNIps as the base platform for laboratory databases, institutional repository, and integrated databases. We are also expecting a global dissemination of XooNIps (http://xoonips.sourceforge.jp/). Concierge is a personal database solution of the researcher, by the researcher, for the researches, which is available as freeware (http://concierge.sourceforge.jp/). It includes features such as laboratory notebook, paper management where PDF files are managed together with information such as bibliographic metadata retrieved with the help of its PubMed ID, manage experimental files with information on experimental conditions, and using its feature to link with XooNIps, files can be easily uploaded to an open database. Samurai Graph: Graphical representation of experiment data is a work that no researcher can avoid. Commercially available graph-plotting tools are not compatible to each other. In order to deal with this issue we have developed the Samurai Graph, also available as a freeware (http://samurai-graph.sourceforge.jp/index.html.en). Researchers can easily create and edit graphs on-screen. The Samurai Graph site has been accessed hundreds of thousands of times, and has received much praise from many users. As Samurai Graph is Java-based it is available on all platforms providing Java support. 3D-SE Viewer is a visualization tool based on a spherical embedding method. We have published the BSI-Team Map as an example of its application on the BSI webpage (http://www.brain.riken.jp/). Here, laboratory heads are positioned in the outer sphere, and keywords on the inner sphere, where the nodes are optimally positioned according to the similarity between each other. It can be rotated or zoomed in or out using the mouse, and laboratories can be searched by clicking the nodes. In the future, application of the 3D-SE Viewer for the visualization of the contents of Neuroinformatics platforms in J-Node, as well as of databases of papers published by BSI researchers is expected. In addition, the PubMed Plus committee of the Society for Neuroscience (SfN) is considering the development of a new tool for the visualization of the abstracts presented at the SfN annual meeting. Conference: Neuroinformatics 2008, Stockholm, Sweden, 7 Sep - 9 Sep, 2008. Presentation Type: Poster Presentation Topic: General Neuroinformatics Citation: Usui S, Okumura Y, Kannon T and Kamiji LN (2008). Neuroinformatics support tools: XooNIps, Concierge, Samurai Graph and 3D-SE Viewer. Front. Neuroinform. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.005 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 25 Jul 2008; Published Online: 25 Jul 2008. * Correspondence: Shiro Usui, RIKEN Brain Science Institute, Tokyo, Tokyo, Japan, usuishiro@riken.jp Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract Supplemental Data The Authors in Frontiers Shiro Usui Yoshihiro Okumura Takayuki Kannon Liuji N Kamiji Google Shiro Usui Yoshihiro Okumura Takayuki Kannon Liuji N Kamiji Google Scholar Shiro Usui Yoshihiro Okumura Takayuki Kannon Liuji N Kamiji PubMed Shiro Usui Yoshihiro Okumura Takayuki Kannon Liuji N Kamiji Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.